Boolean Modifier fails or makes object disappear
It appears that your mesh with the Boolean modifier is a 2-dimensional plane, this will cause some issues with your Boolean operations. I noticed some very unusual behavior when trying to perform a Boolean operation on a 2-dimensional mesh (final result, difference mesh  has been deleted):



However if I extruded the plane a small amount, the result was completely normal:



I think you will have to add some thickness to your mesh before using the Boolean modifier if you want to achieve expected results.

Also see this answer to a very similar question.